[Bioperl-l] Bio::DB::SeqFeature::Store::memory -> filter_by_type very slow

Chris Fields cjfields at illinois.edu
Mon Feb 1 08:23:02 EST 2010


Jelle,

Seems reasonable, but Lincoln and Scott know that code better and are better suited to comment on it. Lincoln, Scott?

chris

On Feb 1, 2010, at 6:24 AM, Jelle Scholtalbers wrote:

> Hi,
> I used the Bio::DB::SeqFeature::Store::memory module to load in a GFF3 file
> which I could then use in my script in a 'queryable' way. To retrieve
> features I used for example
>       $db->features(-type => 'BAC:FPC', -seq_id=>'chromosome0')
> However when doing a profile on my script I found out that 60% of the
> running time went into filter_by_type from
> Bio::DB::SeqFeature::Store::memory.
> Replacing this function with
>    my @features = grep{$_->type eq 'BAC:FPC'}
> $db->features(-seq_id=>'chromosome0')
> which gave me the same results was just a fraction of the earlier run time.
> My script went from 60min. to 4min. for the same result and only changing
> this function (is called often).
> Can/Should this be fixed or is this just the faster way to do it?
> 
> Cheers,
> Jelle
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